Identification of genome size and heterozygosity in 510 Jujube (Ziziphus jujuba Mill.) germplasms based on deep resequencing

Abstract

Introduction Genome size and heterozygosity represent the fundamental genetic attributes of a species, but their intraspecies diversity and evolution remain largely elusive. Methods To address this, we developed a deep-resequencing-based approach for genome estimation by optimizing resequencing depth (30×) and kmer value (21) in Chinese jujube (Ziziphus jujuba Mill.) to achieve the best balance among accuracy, stability, and cost. Using this optimized pipeline, we estimated genome size and heterozygosity across a large panel of jujube accessions. Results We estimated the genome size of 296 cultivated jujube genotypes from 293 to 409 Mb (mean 347 Mb, CV 5.94%) with heterozygosity of 1.30% to 2.01% (mean 1.72%, CV 8.21%); for 214 wild jujube, genome size varies between 311 and 391 Mb (mean 339 Mb, CV 3.40%), and heterozygosity 1.22% to 2.13% (mean 1.74%, CV 6.79%). Additionally, analyzing 798 jujube accessions with resequencing data in NCBI (using k-mer 21) revealed that low sequencing depths (10∼20×) of most accessions (98.61%) results in underestimated genome sizes (4.30–309 Mb) and overestimated heterozygosity (2.17-11.8%). Shannon-Wiener Index analysis for genome heterozygosity and size in jujube indicate a medium diversity level with cultivated jujube higher that wild one. Both genome size and heterozygosity show normal distribution, and there is a significant negative correlation between them. Discussion During domestication from wild to cultivated jujube, average genome size increased by 8 Mb, while heterozygosity slightly decreased. A reference standard for genome size and heterozygosity is proposed and jujube is characterized as a small genome with mediumtohigh heterozygosity. This study establishes a powerful approach for estimating genome characteristics, enriched genomic resources for jujube, and provides insights for plant intraspecific genome diversity and evolution.